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Xu J, Zhang J, Dong Y, Luo Y, Xie W. Effects of polyethylene microplastics on CHCl 3 and CHBr 3 fluxes and microbial community in temperate salt marsh soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124719. [PMID: 39142428 DOI: 10.1016/j.envpol.2024.124719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/03/2024] [Accepted: 08/11/2024] [Indexed: 08/16/2024]
Abstract
Microplastics (MPs) affect the carbon cycle in coastal salt marsh soils. However, studies on their effects on CHCl3 and CHBr3, which are volatile halohydrocarbons that can damage the ozone layer, are lacking. In this study, indoor simulation experiments were conducted to explore the effects of MPs invasion on the source and sink characteristics of soil CHCl3 and CHBr3. The results showed that different concentrations of polyethylene (PE)-MPs promoted CHCl3 and CHBr3 emissions. Emission peaks of the two gases appeared on days 3 and 15 during the culture cycle. CHCl3 and CHBr3 fluxes were mainly affected by soil physicochemical properties and microbial communities. PE-MPs caused changes in soil properties, microorganisms, and related functional genes. Soil total organic carbon, which was significantly and positively correlated with CHCl3. Dissolved organic matter, which was one of the main factors affecting CHBr3, its relative content increased after the addition of PE-MPs. The abundances of Methylocella and Dehalococcoides, which mediate dechlorination reduction, decreased with the addition of PE-MPs. The addition of PE-MPs also significantly varied the abundance of ctrA, which controls dechlorination in soil microorganisms. The gene pceA greatly influenced CHCl3 emissions. In addition, CHBr3 flux was influenced by the interactions between sediment redox and microbial co-metabolic reactions under the control of genes such as TC.FEV.OM and soxB. This study provides theoretical and data support for the source and sink characteristics of volatile halohydrocarbons in coastal salt marshes and highlights the environmental hazards of MPs.
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Affiliation(s)
- Jianing Xu
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Jiale Zhang
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Yange Dong
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Yue Luo
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Wenxia Xie
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China.
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2
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Yadav P, Kumari SP, Hooda S, Gupta RK, Diwan P. Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 369:122342. [PMID: 39232318 DOI: 10.1016/j.jenvman.2024.122342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 08/09/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%-16%), aminoglycosides (7%-9%), multi-drug (5%-9%), and rifampin (3%-9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.
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Affiliation(s)
- Prerna Yadav
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India
| | - Shashi Prabha Kumari
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sunila Hooda
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India
| | - Rakesh Kumar Gupta
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India
| | - Prerna Diwan
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India.
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Baruah M, Gogoi M, Chandra Boro R, Barooah M. Priestia aryabhattai MBM3-Mediated Enhancement of Sulphur Metabolism in Brassica campestris. Curr Microbiol 2024; 81:316. [PMID: 39164526 DOI: 10.1007/s00284-024-03844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/13/2024] [Indexed: 08/22/2024]
Abstract
Sulphur, an essential element for plant growth, is vital for synthesizing various crucial components such as amino acids and enzymes. Its limited availability in acidic soil inhibits crop development and yield. Our research identified low pH tolerance sulphur-metabolizing bacterial isolate Priestia aryabhattai MBM3, with plant growth-promoting traits. Key sulphur-metabolizing genes viz., cysK, cysE, luxS, and a hypothetical gene, BG04-4883 were increasingly upregulated during the lag phase in acidic environments, indicating to the isolates ability to accumulate sulphur through increased activity of these essential genes. Microcosm experiment revealed bioprimed Brassica campestris L seeds with Priestia aryabhattai MBM3 had improved performance in acidic conditions, as demonstrated by agronomic and physiological, and no metabolic demand for sulphur, unlike control untreated plants which showed requirement for sulphur with significant expression of sulfate transporters, as revealed by molecular studies.
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Affiliation(s)
- Manjistha Baruah
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Manuranjan Gogoi
- Department of Tea Husbandry and Technology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Madhumita Barooah
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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Willard DJ, H. Manesh MJ, Bing RG, Alexander BH, Kelly RM. Phenotype-driven assessment of the ancestral trajectory of sulfur biooxidation in the thermoacidophilic archaea Sulfolobaceae. mBio 2024; 15:e0103324. [PMID: 38953360 PMCID: PMC11323534 DOI: 10.1128/mbio.01033-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
Certain members of the family Sulfolobaceae represent the only archaea known to oxidize elemental sulfur, and their evolutionary history provides a framework to understand the development of chemolithotrophic growth by sulfur oxidation. Here, we evaluate the sulfur oxidation phenotype of Sulfolobaceae species and leverage comparative genomic and transcriptomic analysis to identify the key genes linked to sulfur oxidation. Metabolic engineering of the obligate heterotroph Sulfolobus acidocaldarius revealed that the known cytoplasmic components of sulfur oxidation alone are not sufficient to drive prolific sulfur oxidation. Imaging analysis showed that Sulfolobaceae species maintain proximity to the sulfur surface but do not necessarily contact the substrate directly. This indicates that a soluble form of sulfur must be transported to initiate cytoplasmic sulfur oxidation. Conservation patterns and transcriptomic response implicate an extracellular tetrathionate hydrolase and putative thiosulfate transporter in a newly proposed mechanism of sulfur acquisition in the Sulfolobaceae.IMPORTANCESulfur is one of the most abundant elements on earth (2.9% by mass), so it makes sense that the earliest biology found a way to use sulfur to create and sustain life. However, beyond evolutionary significance, sulfur and the molecules it comprises have important technological significance, not only in chemicals such as sulfuric acid and in pyritic ores containing critical metals but also as a waste product from oil and gas production. The thermoacidophilic Sulfolobaceae are unique among the archaea as sulfur oxidizers. The trajectory for how sulfur biooxidation arose and evolved can be traced using experimental and bioinformatic analyses of the available genomic data set. Such analysis can also inform the process by which extracellular sulfur is acquired and transported by thermoacidophilic archaea, a phenomenon that is critical to these microorganisms but has yet to be elucidated.
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Affiliation(s)
- Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Mohamad J. H. Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Benjamin H. Alexander
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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Tothero GK, Hoover RL, Farag IF, Kaplan DI, Weisenhorn P, Emerson D, Chan CS. Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon. Appl Environ Microbiol 2024:e0059924. [PMID: 39133000 DOI: 10.1128/aem.00599-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
Leptothrix ochracea creates distinctive iron-mineralized mats that carpet streams and wetlands. Easily recognized by its iron-mineralized sheaths, L. ochracea was one of the first microorganisms described in the 1800s. Yet it has never been isolated and does not have a complete genome sequence available, so key questions about its physiology remain unresolved. It is debated whether iron oxidation can be used for energy or growth and if L. ochracea is an autotroph, heterotroph, or mixotroph. To address these issues, we sampled L. ochracea-rich mats from three of its typical environments (a stream, wetlands, and a drainage channel) and reconstructed nine high-quality genomes of L. ochracea from metagenomes. These genomes contain iron oxidase genes cyc2 and mtoA, showing that L. ochracea has the potential to conserve energy from iron oxidation. Sox genes confer potential to oxidize sulfur for energy. There are genes for both carbon fixation (RuBisCO) and utilization of sugars and organic acids (acetate, lactate, and formate). In silico stoichiometric metabolic models further demonstrated the potential for growth using sugars and organic acids. Metatranscriptomes showed a high expression of genes for iron oxidation; aerobic respiration; and utilization of lactate, acetate, and sugars, as well as RuBisCO, supporting mixotrophic growth in the environment. In summary, our results suggest that L. ochracea has substantial metabolic flexibility. It is adapted to iron-rich, organic carbon-containing wetland niches, where it can thrive as a mixotrophic iron oxidizer by utilizing both iron oxidation and organics for energy generation and both inorganic and organic carbon for cell and sheath production. IMPORTANCE Winogradsky's observations of L. ochracea led him to propose autotrophic iron oxidation as a new microbial metabolism, following his work on autotrophic sulfur-oxidizers. While much culture-based research has ensued, isolation proved elusive, so most work on L. ochracea has been based in the environment and in microcosms. Meanwhile, the autotrophic Gallionella became the model for freshwater microbial iron oxidation, while heterotrophic and mixotrophic iron oxidation is not well-studied. Ecological studies have shown that Leptothrix overtakes Gallionella when dissolved organic carbon content increases, demonstrating distinct niches. This study presents the first near-complete genomes of L. ochracea, which share some features with autotrophic iron oxidizers, while also incorporating heterotrophic metabolisms. These genome, metabolic modeling, and transcriptome results give us a detailed metabolic picture of how the organism may combine lithoautotrophy with organoheterotrophy to promote Fe oxidation and C cycling and drive many biogeochemical processes resulting from microbial growth and iron oxyhydroxide formation in wetlands.
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Affiliation(s)
- Gracee K Tothero
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Rene L Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Ibrahim F Farag
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - Daniel I Kaplan
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
| | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Clara S Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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Khan IU, Saqib M, Amin A, Manzoor S, Ahmed I, Liu RR, Jiao JY, Zhi XY, Li WJ. Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China. Antonie Van Leeuwenhoek 2024; 117:103. [PMID: 39042225 DOI: 10.1007/s10482-024-02001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/09/2024] [Indexed: 07/24/2024]
Abstract
Genus Thermus is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus Thermus in geographically different thermal springs. Sixteen Thermus strains were isolated and sequenced from hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of 971 Orthologous Protein Families (supermatrix and gene content methods) revealed a mixed distribution of the Thermus strains. Whole genome based phylogenetic analysis showed, all 16 Thermus strains belong to five species; Thermus oshimai (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), Thermus antranikianii (YIM 73052, 77412, 77311, 71206), Thermus brokianus (YIM 73518, 71318, 72351), Thermus hydrothermalis (YIM 730264 and 77927) and one potential novel species 77420 forming clade with Thermus thalpophilus SYSU G00506T. Although the genomes of different strains of Thermus of same species were highly similar in their metabolic pathways, but subtle differences were found. CRISPR loci were detected through genome-wide screening, which showed that Thermus isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the Thermus genomes which could be helpful to acquire DNA from environment. In the present study it was found that Thermus isolates use two mechanism of incomplete denitrification pathway, some Thermus strains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of Thermus genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of T. oshimai and T. antranikianii strains, while genomes of all T. brokianus strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced Thermus strains. Strains 77,420, 77,311, 73,518, 77,412 and 72,351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy. Through the comparative genomic analysis, we also identified 77420 as the genome type species and its validity as novel organism was confirmed by whole genome sequences comparison. Although isolate 77420 had 99.0% 16S rRNA gene sequence similarity with T. thalpophilus SYSU G00506T but based on ANI 95.86% (Jspecies) and digital DDH 68.80% (GGDC) values differentiate it as a potential novel species. Similarly, in the phylogenomic tree, the novel isolate 77,420 forming a separate branch with their closest reference type strain T. thalpophilus SYSU G00506T.
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Affiliation(s)
- Inam Ullah Khan
- Faculty of Veterinary and Animal Sciences, Institute of Microbiology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, 29050, Pakistan
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Muhammad Saqib
- Department of Zoology, Gomal University, Tank Campus, 29050, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, 45500, Pakistan
| | - Sadia Manzoor
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Iftikhar Ahmed
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Rui-Rui Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Yang Zhi
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
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Twible LE, Whaley-Martin K, Chen LX, Colenbrander Nelson T, Arrey JL, Jarolimek CV, King JJ, Ramilo L, Sonnenberg H, Banfield JF, Apte SC, Warren LA. pH and thiosulfate dependent microbial sulfur oxidation strategies across diverse environments. Front Microbiol 2024; 15:1426584. [PMID: 39101034 PMCID: PMC11294248 DOI: 10.3389/fmicb.2024.1426584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
Sulfur oxidizing bacteria (SOB) play a key role in sulfur cycling in mine tailings impoundment (TI) waters, where sulfur concentrations are typically high. However, our understanding of SOB sulfur cycling via potential S oxidation pathways (sox, rdsr, and S4I) in these globally ubiquitous contexts, remains limited. Here, we identified TI water column SOB community composition, metagenomics derived metabolic repertoires, physicochemistry, and aqueous sulfur concentration and speciation in four Canadian base metal mine, circumneutral-alkaline TIs over four years (2016 - 2019). Identification and examination of genomes from nine SOB genera occurring in these TI waters revealed two pH partitioned, metabolically distinct groups, which differentially influenced acid generation and sulfur speciation. Complete sox (csox) dominant SOB (e.g., Halothiobacillus spp., Thiomonas spp.) drove acidity generation and S2O3 2- consumption via the csox pathway at lower pH (pH ~5 to ~6.5). At circumneutral pH conditions (pH ~6.5 to ~8.5), the presence of non-csox dominant SOB (hosting the incomplete sox, rdsr, and/or other S oxidation reactions; e.g. Thiobacillus spp., Sulfuriferula spp.) were associated with higher [S2O3 2-] and limited acidity generation. The S4I pathway part 1 (tsdA; S2O3 2- to S4O6 2-), was not constrained by pH, while S4I pathway part 2 (S4O6 2- disproportionation via tetH) was limited to Thiobacillus spp. and thus circumneutral pH values. Comparative analysis of low, natural (e.g., hydrothermal vents and sulfur hot springs) and high (e.g., Zn, Cu, Pb/Zn, and Ni tailings) sulfur systems literature data with these TI results, reveals a distinct TI SOB mining microbiome, characterized by elevated abundances of csox dominant SOB, likely sustained by continuous replenishment of sulfur species through tailings or mining impacted water additions. Our results indicate that under the primarily oxic conditions in these systems, S2O3 2- availability plays a key role in determining the dominant sulfur oxidation pathways and associated geochemical and physicochemical outcomes, highlighting the potential for biological management of mining impacted waters via pH and [S2O3 2-] manipulation.
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Affiliation(s)
- Lauren E. Twible
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Kelly Whaley-Martin
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | | | - James L.S. Arrey
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Chad V. Jarolimek
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Josh J. King
- Commonwealth Scientific Industrial and Research Organization, Black Mountain, ACT, Australia
| | | | | | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | - Simon C. Apte
- Commonwealth Scientific Industrial and Research Organization, Clayton, VIC, Australia
| | - Lesley A. Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
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Wang Z, Digel L, Yuan Y, Lu H, Yang Y, Vogt C, Richnow HH, Nielsen LP. Electrogenic sulfur oxidation mediated by cable bacteria and its ecological effects. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 20:100371. [PMID: 38283867 PMCID: PMC10821171 DOI: 10.1016/j.ese.2023.100371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/30/2024]
Abstract
At the sediment-water interfaces, filamentous cable bacteria transport electrons from sulfide oxidation along their filaments towards oxygen or nitrate as electron acceptors. These multicellular bacteria belonging to the family Desulfobulbaceae thus form a biogeobattery that mediates redox processes between multiple elements. Cable bacteria were first reported in 2012. In the past years, cable bacteria have been found to be widely distributed across the globe. Their potential in shaping the surface water environments has been extensively studied but is not fully elucidated. In this review, the biogeochemical characteristics, conduction mechanisms, and geographical distribution of cable bacteria, as well as their ecological effects, are systematically reviewed and discussed. Novel insights for understanding and applying the role of cable bacteria in aquatic ecology are summarized.
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Affiliation(s)
- Zhenyu Wang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Leonid Digel
- Center for Electromicrobiology, Department of Biology, Aarhus University, DK-8000, Aarhus, Denmark
| | - Yongqiang Yuan
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yonggang Yang
- School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510007, China
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Lars Peter Nielsen
- Center for Electromicrobiology, Department of Biology, Aarhus University, DK-8000, Aarhus, Denmark
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Sudo M, Osvatic J, Taylor JD, Dufour SC, Prathep A, Wilkins LGE, Rattei T, Yuen B, Petersen JM. SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers. mSystems 2024; 9:e0113523. [PMID: 38747602 PMCID: PMC11237559 DOI: 10.1128/msystems.01135-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/13/2024] [Indexed: 06/19/2024] Open
Abstract
Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of soxY in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical" soxY were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent soxY genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the soxY gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.
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Affiliation(s)
- Marta Sudo
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jay Osvatic
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - John D. Taylor
- Life Sciences, The Natural History Museum, London, United Kingdom
| | - Suzanne C. Dufour
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Anchana Prathep
- Department of Biology, Faculty of Science, Prince of Songkla University, HatYai, Thailand
| | - Laetitia G. E. Wilkins
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Rattei
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Benedict Yuen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jillian M. Petersen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
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10
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Kabir SF, Sundar SV, Robles A, Miranda EM, Delgado AG, Fini EH. Microbially Mediated Rubber Recycling to Facilitate the Valorization of Scrap Tires. Polymers (Basel) 2024; 16:1017. [PMID: 38611275 PMCID: PMC11013845 DOI: 10.3390/polym16071017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
The recycling of scrap tire rubber requires high levels of energy, which poses challenges to its proper valorization. The application of rubber in construction requires significant mechanical and/or chemical treatment of scrap rubber to compatiblize it with the surrounding matrix. These methods are energy-consuming and costly and may lead to environmental concerns associated with chemical leachates. Furthermore, recent methods usually call for single-size rubber particles or a narrow rubber particle size distribution; this, in turn, adds to the pre-processing cost. Here, we used microbial etching (e.g., microbial metabolism) to modify the surface of rubber particles of varying sizes. Specifically, we subjected rubber particles with diameters of 1.18 mm and 0.6 mm to incubation in flask bioreactors containing a mineral medium with thiosulfate and acetate and inoculated them with a microbial culture from waste-activated sludge. The near-stoichiometric oxidation of thiosulfate to sulfate was observed in the bioreactors. Most notably, two of the most potent rubber-degrading bacteria (Gordonia and Nocardia) were found to be significantly enriched in the medium. In the absence of added thiosulfate in the medium, sulfate production, likely from the desulfurization of the rubber, was also observed. Microbial etching increased the surface polarity of rubber particles, enhancing their interactions with bitumen. This was evidenced by an 82% reduction in rubber-bitumen separation when 1.18 mm microbially etched rubber was used. The study outcomes provide supporting evidence for a rubber recycling method that is environmentally friendly and has a low cost, promoting pavement sustainability and resource conservation.
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Affiliation(s)
- Sk Faisal Kabir
- School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ 85281, USA
- Center for Research and Education in Advanced Transportation Engineering Systems (CREATEs), Rowan University, South Jersey Technology Park, 107 Gilbreth Parkway, Mullica Hill, NJ 08062, USA
| | - Skanda Vishnu Sundar
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA (E.M.M.)
- School for Engineering of Matter, Transport & Energy, Arizona State University, 501 E Tyler Mall, Tempe, AZ 85287, USA
| | - Aide Robles
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA (E.M.M.)
- School for Engineering of Matter, Transport & Energy, Arizona State University, 501 E Tyler Mall, Tempe, AZ 85287, USA
| | - Evelyn M. Miranda
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA (E.M.M.)
- School for Engineering of Matter, Transport & Energy, Arizona State University, 501 E Tyler Mall, Tempe, AZ 85287, USA
| | - Anca G. Delgado
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA (E.M.M.)
- School for Engineering of Matter, Transport & Energy, Arizona State University, 501 E Tyler Mall, Tempe, AZ 85287, USA
| | - Elham H. Fini
- School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ 85281, USA
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11
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Iizuka R, Hattori S, Kosaka Y, Masaki Y, Kawano Y, Ohtsu I, Hibbett D, Katayama Y, Yoshida M. Sulfur assimilation using gaseous carbonyl sulfide by the soil fungus Trichoderma harzianum. Appl Environ Microbiol 2024; 90:e0201523. [PMID: 38299812 PMCID: PMC10880591 DOI: 10.1128/aem.02015-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024] Open
Abstract
Fungi have the capacity to assimilate a diverse range of both inorganic and organic sulfur compounds. It has been recognized that all sulfur sources taken up by fungi are in soluble forms. In this study, we present evidence that fungi can utilize gaseous carbonyl sulfide (COS) for the assimilation of a sulfur compound. We found that the filamentous fungus Trichoderma harzianum strain THIF08, which has constitutively high COS-degrading activity, was able to grow with COS as the sole sulfur source. Cultivation with 34S-labeled COS revealed that sulfur atom from COS was incorporated into intracellular metabolites such as glutathione and ergothioneine. COS degradation by strain THIF08, in which as much of the moisture derived from the agar medium as possible was removed, indicated that gaseous COS was taken up directly into the cell. Escherichia coli transformed with a COS hydrolase (COSase) gene, which is clade D of the β-class carbonic anhydrase subfamily enzyme with high specificity for COS but low activity for CO2 hydration, showed that the COSase is involved in COS assimilation. Comparison of sulfur metabolites of strain THIF08 revealed a higher relative abundance of reduced sulfur compounds under the COS-supplemented condition than the sulfate-supplemented condition, suggesting that sulfur assimilation is more energetically efficient with COS than with sulfate because there is no redox change of sulfur. Phylogenetic analysis of the genes encoding COSase, which are distributed in a wide range of fungal taxa, suggests that the common ancestor of Ascomycota, Basidiomycota, and Mucoromycota acquired COSase at about 790-670 Ma.IMPORTANCEThe biological assimilation of gaseous CO2 and N2 involves essential processes known as carbon fixation and nitrogen fixation, respectively. In this study, we found that the fungus Trichoderma harzianum strain THIF08 can grow with gaseous carbonyl sulfide (COS), the most abundant and ubiquitous gaseous sulfur compound, as a sulfur source. When the fungus grew in these conditions, COS was assimilated into sulfur metabolites, and the key enzyme of this assimilation process is COS hydrolase (COSase), which specifically degrades COS. Moreover, the pathway was more energy efficient than the typical sulfate assimilation pathway. COSase genes are widely distributed in Ascomycota, Basidiomycota, and Mucoromycota and also occur in some Chytridiomycota, indicating that COS assimilation is widespread in fungi. Phylogenetic analysis of these genes revealed that the acquisition of COSase in filamentous fungi was estimated to have occurred at about 790-670 Ma, around the time that filamentous fungi transitioned to a terrestrial environment.
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Affiliation(s)
- Ryuka Iizuka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Shohei Hattori
- International Center for Isotope Effects Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu, China
| | - Yusuke Kosaka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yoshihito Masaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yusuke Kawano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Euglena Co., Ltd., Minato‑ku, Tokyo, Japan
| | - Iwao Ohtsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Euglena Co., Ltd., Minato‑ku, Tokyo, Japan
| | - David Hibbett
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- Independent Administrative Institution, Tokyo National Research Institute for Cultural Properties, Taito-ku, Tokyo, Japan
| | - Makoto Yoshida
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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12
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Cai R, Li R, Cao X, Xu C. Available sulfur and phosphorus transformation mechanism and functional microorganisms during sheep manure composting on Qinghai-Tibet Plateau under two moisture contents. BIORESOURCE TECHNOLOGY 2024; 394:130191. [PMID: 38081470 DOI: 10.1016/j.biortech.2023.130191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 02/04/2024]
Abstract
Understanding the mechanisms of sulfur and phosphorus transformation during composting is important for improving compost fertility. This study aims to investigate the microbial mechanism of available sulfur and phosphorus transformation during sheep manure composting under different moisture contents (45%: M45 and 60%: M60) on the Qinghai-Tibet Plateau using metagenomics technology. The results showed that the final available sulfur and phosphorus contents of M45 were 11% and 13% higher than those of M60, respectively. M45 enhanced sulfur oxidation, sulfate reduction, and thiosulfate disproportionation. These steps were significantly positively correlated with available sulfur, and Pseudomonas, Thermobifida, Luteimonas, Brevibacterium, Planifilum, and Xinfangfangia were the main participants. Available phosphorus was significantly positively correlated with polyphosphate degradation and inorganic P solubilization, and the main participants in these steps were Luteimonas, Brachybacterium, Corynebacterium, Jeotgalicoccus, Microbacterium, Streptomyces, and Pseudoxanthomonas. These findings reveal the microbial mechanisms of available and phosphorus transformation during composting at two moisture contents.
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Affiliation(s)
- Rui Cai
- College of Engineering, China Agricultural University, Beijing 100083, China; School of Environmental Science & Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei Province 430074, China
| | - Rongrong Li
- College of Environment and Life Sciences, Weinan Normal University, Weinan, Shaanxi Province 714099, China
| | - Xiaohui Cao
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Chuncheng Xu
- College of Engineering, China Agricultural University, Beijing 100083, China.
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13
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Lages MA, do Vale A, Lemos ML, Balado M. Remodulation of bacterial transcriptome after acquisition of foreign DNA: the case of irp-HPI high-pathogenicity island in Vibrio anguillarum. mSphere 2024; 9:e0059623. [PMID: 38078732 PMCID: PMC10826351 DOI: 10.1128/msphere.00596-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024] Open
Abstract
The high-pathogenicity island irp-HPI is widespread in Vibrionaceae and encodes the siderophore piscibactin, as well as the regulator PbtA that is essential for its expression. In this work, we aim to study whether PbtA directly interacts with irp-HPI promoters. Furthermore, we hypothesize that PbtA, and thereby the acquisition of irp-HPI island, may also influence the expression of other genes elsewhere in the bacterial genome. To address this question, an RNAseq analysis was conducted to identify differentially expressed genes after pbtA deletion in Vibrio anguillarum RV22 genetic background. The results showed that PbtA not only modulates the irp-HPI genes but also modulates the expression of a plethora of V. anguillarum core genome genes, inducing nitrate, arginine, and sulfate metabolism, T6SS1, and quorum sensing, while repressing lipopolysaccharide (LPS) production, MARTX toxin, and major porins such as OmpV and ChiP. The direct binding of the C-terminal domain of PbtA to piscibactin promoters (PfrpA and PfrpC), quorum sensing (vanT), LPS transporter wza, and T6SS structure- and effector-encoding genes was demonstrated by electrophoretic mobility shift assay (EMSA). The results provide valuable insights into the regulatory mechanisms underlying the expression of irp-HPI island and its impact on Vibrios transcriptome, with implications in pathogenesis.IMPORTANCEHorizontal gene transfer enables bacteria to acquire traits, such as virulence factors, thereby increasing the risk of the emergence of new pathogens. irp-HPI genomic island has a broad dissemination in Vibrionaceae and is present in numerous potentially pathogenic marine bacteria, some of which can infect humans. Previous works showed that certain V. anguillarum strains exhibit an expanded host range plasticity and heightened virulence, a phenomenon linked to the acquisition of the irp-HPI genomic island. The present work shows that this adaptive capability is likely achieved through comprehensive changes in the transcriptome of the bacteria and that these changes are mediated by the master regulator PbtA encoded within the irp-HPI element. Our results shed light on the broad implications of horizontal gene transfer in bacterial evolution, showing that the acquired DNA can directly mediate changes in the expression of the core genome, with profounds implications in pathogenesis.
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Affiliation(s)
- Marta A. Lages
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Manuel L. Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
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14
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Kanao T. Tetrathionate hydrolase from the acidophilic microorganisms. Front Microbiol 2024; 15:1338669. [PMID: 38348185 PMCID: PMC10859504 DOI: 10.3389/fmicb.2024.1338669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Tetrathionate hydrolase (TTH) is a unique enzyme found in acidophilic sulfur-oxidizing microorganisms, such as bacteria and archaea. This enzyme catalyzes the hydrolysis of tetrathionate to thiosulfate, elemental sulfur, and sulfate. It is also involved in dissimilatory sulfur oxidation metabolism, the S4-intermediate pathway. TTHs have been purified and characterized from acidophilic autotrophic sulfur-oxidizing microorganisms. All purified TTHs show an optimum pH in the acidic range, suggesting that they are localized in the periplasmic space or outer membrane. In particular, the gene encoding TTH from Acidithiobacillus ferrooxidans (Af-tth) was identified and recombinantly expressed in Escherichia coli cells. TTH activity could be recovered from the recombinant inclusion bodies by acid refolding treatment for crystallization. The mechanism of tetrathionate hydrolysis was then elucidated by X-ray crystal structure analysis. Af-tth is highly expressed in tetrathionate-grown cells but not in iron-grown cells. These unique structural properties, reaction mechanisms, gene expression, and regulatory mechanisms are discussed in this review.
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Affiliation(s)
- Tadayoshi Kanao
- Department of Agricultural and Biological Chemistry, Graduate School of Environment, Life, Natural Science, and Technology, Okayama University, Okayama, Japan
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15
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Valentin-Alvarado LE, Fakra SC, Probst AJ, Giska JR, Jaffe AL, Oltrogge LM, West-Roberts J, Rowland J, Manga M, Savage DF, Greening C, Baker BJ, Banfield JF. Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism. MICROBIOME 2024; 12:15. [PMID: 38273328 PMCID: PMC10811913 DOI: 10.1186/s40168-023-01704-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 10/18/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. RESULTS Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. CONCLUSIONS Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.
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Affiliation(s)
- Luis E Valentin-Alvarado
- Graduate Group in Microbiology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Sirine C Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexander J Probst
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry,, University of Duisburg-Essen, Essen, Essen, Germany
| | - Jonathan R Giska
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- Cleaner Air Oregon Program, Oregon Department of Environmental Quality, Portland, USA
| | - Alexander L Jaffe
- Graduate Group in Microbiology, University of California, Berkeley, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Jacob West-Roberts
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Joel Rowland
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- Earth and Env. Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Michael Manga
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Brett J Baker
- Department of Integrative Biology, University of Texas, Austin, USA
- Department of Marine Science, University of Texas, Austin, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Marine Science, University of Texas, Austin, USA.
- Energy Geoscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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16
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Yuan X, Sun Y, Ni D, Xie Z, Zhang Y, Miao S, Wu L, Xing X, Zuo J. A biological strategy for sulfide control in sewers: Removing sulfide by sulfur-oxidizing bacteria. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119237. [PMID: 37832290 DOI: 10.1016/j.jenvman.2023.119237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/16/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023]
Abstract
Sulfide produced from sewers is considered one of the dominant threats to public health and sewer lifespan due to its toxicity and corrosiveness. In this study, we developed an environmentally friendly strategy for gaseous sulfide control by enriching indigenous sulfur-oxidizing bacteria (SOB) from sewer sediment. Ceramics acted as bio-carriers for immobilizing SOB for practical use in a lab-scale sewer reactor. 16 S rRNA gene sequences revealed that the SOB consortium was successfully enriched, with Thiobacillus, Pseudomonas, and Alcaligenes occupying a dominant abundance of 64.7% in the microbial community. Metabolic pathway analysis in different acclimatization stages indicates that microorganisms could convert thiosulfate and sulfide into elemental sulfur after enrichment and immobilization. A continuous experiment in lab-scale sewer reactors confirmed an efficient result for sulfide removal with hydrogen sulfide reduction of 43.9% and 85.1% under high-sulfur load and low-sulfur load conditions, respectively. This study shed light on the promising application for sewer sulfide control by biological sulfur oxidation strategy.
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Affiliation(s)
- Xin Yuan
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Research Institute of Highway Ministry of Transport, Beijing 100088, China
| | - Yiquan Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Dong Ni
- Research Institute of Highway Ministry of Transport, Beijing 100088, China
| | - Zhenwen Xie
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanyan Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Sun Miao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Linjun Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xin Xing
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Research Institute of Highway Ministry of Transport, Beijing 100088, China.
| | - Jiane Zuo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China.
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17
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Zhang H, Dou Z, Bi W, Yang C, Wu X, Wang L. Multi-omics study of sulfur metabolism affecting functional microbial community succession during aerobic solid-state fermentation. BIORESOURCE TECHNOLOGY 2023; 387:129664. [PMID: 37573975 DOI: 10.1016/j.biortech.2023.129664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Microbial-mediated sulfur metabolism is closely related to carbon and nitrogen metabolism in natural biological systems. In this study, the effects of sulfur metabolism on microbial communities and functional enzyme succession were investigated based on integrated multi-omics by adding sulfur-containing compounds to aerobic fermentation systems. Sulfur powder was oxidized to S2O32- and subsequently to SO42- by the microbial sulfur-oxidizing system, which lowered the pH to 7.5 on day 7. The decrease in pH resulted in Planifilum (secreted S8, M17 and M32 proteases) losing its competitive advantage, whereas Novibacillus (secreted M14 and M19 metalloproteases) became dominant. Structural proteomics indicated that the surface of Novibacillus proteases has more negatively charged amino acid residues that help maintain protein stability at low pH. These findings aid understanding of the effects of sulfur metabolism on fermentation and the mechanism of microbial adaptation after pH reduction, providing new perspectives on the optimization of fermentation processes.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Zhixin Dou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Wenhui Bi
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Faculty of Food Science and Engineering, Shandong Agricultural and Engineering University, Jinan, Shandong 250100, China
| | - Chuanlun Yang
- Shandong Chambroad Holding Group Co., Ltd., Boxing 256599, China
| | - Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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18
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Zecchin S, Wang J, Martin M, Romani M, Planer-Friedrich B, Cavalca L. Microbial communities in paddy soils: differences in abundance and functionality between rhizosphere and pore water, the influence of different soil organic carbon, sulfate fertilization and cultivation time, and contribution to arsenic mobility and speciation. FEMS Microbiol Ecol 2023; 99:fiad121. [PMID: 37804167 PMCID: PMC10630088 DOI: 10.1093/femsec/fiad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/09/2023] Open
Abstract
Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Although mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear. Here, we tested if original unplanted soil, rhizosphere soil and pore water represented distinct ecological microniches for arsenic-, sulfur- and iron-cycling microorganisms and compared the influence of relevant factors such as soil type, sulfate fertilization and cultivation time. In rice open-air-mesocosms with two paddy soils (2.0% and 4.7% organic carbon), Illumina 16S rRNA gene sequencing demonstrated minor effects of cultivation time and sulfate fertilization that decreased Archaea-driven microbial networks and incremented sulfate-reducing and sulfur-oxidizing bacteria. Different compartments, characterized by different bacterial and archaeal compositions, had the strongest effect, with higher microbial abundances, bacterial biodiversity and interconnections in the rhizosphere vs pore water. Within each compartment, a significant soil type effect was observed. Higher percentage contributions of rhizosphere dissimilatory arsenate- and iron-reducing, arsenite-oxidizing, and, surprisingly, dissimilatory sulfate-reducing bacteria, as well as pore water iron-oxidizing bacteria in the lower organic carbon soil, supported previous chemistry-based interpretations of a more active S-cycling, a higher percentage of thioarsenates and lower arsenic mobility by sorption to mixed Fe(II)Fe(III)-minerals in this soil.
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Affiliation(s)
- Sarah Zecchin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milano-20133, Italy
| | - Jiajia Wang
- Environmental Geochemistry Group, Bayreuth Center for Ecology and Environmental Research (BAYCEER), Bayreuth University, 95440, Germany
| | - Maria Martin
- Department of Agriculture, Forest and Food Science, University of Turin, Turin-10095, Italy
| | - Marco Romani
- Rice Research Centre, Ente Nazionale Risi, Castello d'Agogna, Pavia-27030, Italy
| | - Britta Planer-Friedrich
- Environmental Geochemistry Group, Bayreuth Center for Ecology and Environmental Research (BAYCEER), Bayreuth University, 95440, Germany
| | - Lucia Cavalca
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milano-20133, Italy
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Gao Y, Zhu H, Wang J, Shao Z, Wei S, Wang R, Cheng R, Jiang L. Physiological and Genomic Characterization of a Novel Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium of Genus Thiomicrorhabdus Isolated from a Coastal Sediment. Microorganisms 2023; 11:2569. [PMID: 37894227 PMCID: PMC10608990 DOI: 10.3390/microorganisms11102569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Thiomicrorhabdus species, belonging to the family Piscirickettsiaceae in the phylum Pseudomonadotav are usually detected in various sulfur-rich marine environments. However, only a few bacteria of Thiomicrorhabdus have been isolated, and their ecological roles and environmental adaptations still require further understanding. Here, we report a novel strain, XGS-01T, isolated from a coastal sediment, which belongs to genus Thiomicrorhabdus and is most closely related to Thiomicrorhabdus hydrogeniphila MAS2T, with a sequence similarity of 97.8%. Phenotypic characterization showed that XGS-01T is a mesophilic, sulfur-oxidizing, obligate chemolithoautotrophy, with carbon dioxide as its sole carbon source and oxygen as its sole electron acceptor. During thiosulfate oxidation, strain XGS-01T can produce extracellular sulfur of elemental α-S8, as confirmed via scanning electron microscopy and Raman spectromicroscopy. Polyphasic taxonomy results indicate that strain XGS-01T represents a novel species of the genus Thiomicrorhabdus, named Thiomicrorhabdus lithotrophica sp. nov. Genomic analysis confirmed that XGS-01T performed thiosulfate oxidation through a sox multienzyme complex, and harbored fcc and sqr genes for sulfide oxidation. Comparative genomics analysis among five available genomes from Thiomicrorhabdus species revealed that carbon fixation via the oxidation of reduced-sulfur compounds coupled with oxygen reduction is conserved metabolic pathways among members of genus Thiomicrorhabdus.
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Affiliation(s)
- Yu Gao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
- School of Marine Sciences, China University of Geosciences, Beijing 100083, China
| | - Han Zhu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Jun Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Shiping Wei
- School of Marine Sciences, China University of Geosciences, Beijing 100083, China
| | - Ruicheng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Ruolin Cheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
- School of Marine Biology, Xiamen Ocean Vocational College, Xiamen 361005, China
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20
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Yin X, Li X, Li Q, Wang B, Zheng L. Complete genome analysis reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum. Mar Genomics 2023; 71:101058. [PMID: 37478643 DOI: 10.1016/j.margen.2023.101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/23/2023]
Abstract
One sulfur-oxidizing bacterium Thioclava sp. M1-LQ-LJL-11 was isolated from the gill of Chrysomallon squamiferum collected from 2700 m deep hydrothermal named Longqi on the southwest Indian Ocean ridge. In order to understand its survival mechanism in hydrothermal extreme environment and symbiotic relationship with its host, the complete genome of strain M1-LQ-LJL-11 was sequenced and analyzed. A total of 6117 Mb of valid data was obtained, including 4096 coding genes, 61 non coding genes, including 9 rRNAs (among them, there are 3 in 23S rRNA, 3 in 5S rRNA, and 3 in 16S rRNA.), 52 tRNAs and 35 genomic islands. Strain M1-LQ-LJL-11 contains one chromosome and two plasmids. In the genome annotation information of the strain, we found 28 genes including cys sox, sor, sqr, tst related to sulfur metabolism and 17 metal resistance genes. Interestingly, a pair of quorum sensing system which probably regulating biofilm formation located in chromosome was found. These genes are critical for self-adaptation against severe environment as well as host survival. This study provides a basis understanding for the adaptive strategies of deep-sea hydrothermal bacteria and symbiotic relationship with its host in extreme environments through gene level.
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Affiliation(s)
- Xin Yin
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362200, China
| | - Xiang Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Qian Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Bingshu Wang
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362200, China
| | - Li Zheng
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362200, China; Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China.
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21
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Methner A, Kuzyk SB, Petersen J, Bauer S, Brinkmann H, Sichau K, Wanner G, Wolf J, Neumann-Schaal M, Henke P, Tank M, Spröer C, Bunk B, Overmann J. Thiorhodovibrio frisius and Trv. litoralis spp. nov., Two Novel Members from a Clade of Fastidious Purple Sulfur Bacteria That Exhibit Unique Red-Shifted Light-Harvesting Capabilities. Microorganisms 2023; 11:2394. [PMID: 37894052 PMCID: PMC10609205 DOI: 10.3390/microorganisms11102394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
In the pursuit of cultivating anaerobic anoxygenic phototrophs with unusual absorbance spectra, a purple sulfur bacterium was isolated from the shoreline of Baltrum, a North Sea island of Germany. It was designated strain 970, due to a predominant light harvesting complex (LH) absorption maximum at 963-966 nm, which represents the furthest infrared-shift documented for such complexes containing bacteriochlorophyll a. A polyphasic approach to bacterial systematics was performed, comparing genomic, biochemical, and physiological properties. Strain 970 is related to Thiorhodovibrio winogradskyi DSM 6702T by 26.5, 81.9, and 98.0% similarity via dDDH, ANI, and 16S rRNA gene comparisons, respectively. The photosynthetic properties of strain 970 were unlike other Thiorhodovibrio spp., which contained typical LH absorbing characteristics of 800-870 nm, as well as a newly discovered absorption band at 908 nm. Strain 970 also had a different photosynthetic operon composition. Upon genomic comparisons with the original Thiorhodovibrio strains DSM 6702T and strain 06511, the latter was found to be divergent, with 25.3, 79.1, and 97.5% similarity via dDDH, ANI, and 16S rRNA gene homology to Trv. winogradskyi, respectively. Strain 06511 (=DSM 116345T) is thereby described as Thiorhodovibrio litoralis sp. nov., and the unique strain 970 (=DSM 111777T) as Thiorhodovibrio frisius sp. nov.
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Affiliation(s)
- Anika Methner
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Steven B Kuzyk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Sabine Bauer
- Former Institution: Paläomikrobiologie, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Postfach 2503, 26111 Oldenburg, Germany
| | - Henner Brinkmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Katja Sichau
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Jacqueline Wolf
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Petra Henke
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Marcus Tank
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Former Institution: Paläomikrobiologie, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Postfach 2503, 26111 Oldenburg, Germany
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
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22
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Ibáñez A, Garrido-Chamorro S, Coque JJR, Barreiro C. From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus. Genes (Basel) 2023; 14:1772. [PMID: 37761912 PMCID: PMC10531304 DOI: 10.3390/genes14091772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.
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Affiliation(s)
- Ana Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Área de Investigación Agrícola, 47071 Valladolid, Spain
| | - Sonia Garrido-Chamorro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
| | - Juan J. R. Coque
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
| | - Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
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23
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Sun K, Yu M, Zhu XY, Xue CX, Zhang Y, Chen X, Yao P, Chen L, Fu L, Yang Z, Zhang XH. Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole. Microbiol Spectr 2023; 11:e0114923. [PMID: 37623326 PMCID: PMC10580873 DOI: 10.1128/spectrum.01149-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.
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Affiliation(s)
- Kai Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Min Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Yu Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Lin Chen
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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24
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Madigan MT, Bender KS, Sanguedolce SA, Parenteau MN, Mayer MH, Kimura Y, Wang-Otomo ZY, Sattley WM. Genomic basis for the unique phenotype of the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis. Extremophiles 2023; 27:19. [PMID: 37481751 DOI: 10.1007/s00792-023-01304-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
Although several species of purple sulfur bacteria inhabit soda lakes, Rhodobaca bogoriensis is the first purple nonsulfur bacterium cultured from such highly alkaline environments. Rhodobaca bogoriensis strain LBB1T was isolated from Lake Bogoria, a soda lake in the African Rift Valley. The phenotype of Rhodobaca bogoriensis is unique among purple bacteria; the organism is alkaliphilic but not halophilic, produces carotenoids absent from other purple nonsulfur bacteria, and is unable to grow autotrophically or fix molecular nitrogen. Here we analyze the draft genome sequence of Rhodobaca bogoriensis to gain further insight into the biology of this extremophilic purple bacterium. The strain LBB1T genome consists of 3.91 Mbp with no plasmids. The genome sequence supports the defining characteristics of strain LBB1T, including its (1) production of a light-harvesting 1-reaction center (LH1-RC) complex but lack of a peripheral (LH2) complex, (2) ability to synthesize unusual carotenoids, (3) capacity for both phototrophic (anoxic/light) and chemotrophic (oxic/dark) energy metabolisms, (4) utilization of a wide variety of organic compounds (including acetate in the absence of a glyoxylate cycle), (5) ability to oxidize both sulfide and thiosulfate despite lacking the capacity for autotrophic growth, and (6) absence of a functional nitrogen-fixation system for diazotrophic growth. The assortment of properties in Rhodobaca bogoriensis has no precedent among phototrophic purple bacteria, and the results are discussed in relation to the organism's soda lake habitat and evolutionary history.
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Affiliation(s)
- Michael T Madigan
- School of Biological Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Kelly S Bender
- School of Biological Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Sophia A Sanguedolce
- School of Biological Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Mary N Parenteau
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Marisa H Mayer
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Yukihiro Kimura
- Department of Agrobioscience, Kobe University, Kobe, 657-8501, Japan
| | | | - W Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA.
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25
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Mateos K, Chappell G, Klos A, Le B, Boden J, Stüeken E, Anderson R. The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth. SCIENCE ADVANCES 2023; 9:eade4847. [PMID: 37418533 PMCID: PMC10328410 DOI: 10.1126/sciadv.ade4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/06/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms, regulating the Earth's redox state, and affecting climate. However, geochemical reconstructions of the ancient sulfur cycle are confounded by ambiguous isotopic signals. We use phylogenetic reconciliation to ascertain the timing of ancient sulfur cycling gene events across the tree of life. Our results suggest that metabolisms using sulfide oxidation emerged in the Archean, but those involving thiosulfate emerged only after the Great Oxidation Event. Our data reveal that observed geochemical signatures resulted not from the expansion of a single type of organism but were instead associated with genomic innovation across the biosphere. Moreover, our results provide the first indication of organic sulfur cycling from the Mid-Proterozoic onwards, with implications for climate regulation and atmospheric biosignatures. Overall, our results provide insights into how the biological sulfur cycle evolved in tandem with the redox state of the early Earth.
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Affiliation(s)
- Katherine Mateos
- Carleton College, Northfield, MN, USA
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Garrett Chappell
- Carleton College, Northfield, MN, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aya Klos
- Carleton College, Northfield, MN, USA
| | - Bryan Le
- Carleton College, Northfield, MN, USA
| | - Joanne Boden
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Eva Stüeken
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Rika Anderson
- Carleton College, Northfield, MN, USA
- NASA NExSS Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
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26
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Lu W, Wang L, Liang J, Lu Y, Wang J, Fu YV. Dynamically Quantifying Intracellular Elemental Sulfur and Predicting Pertinent Gene Transcription by Raman Spectroscopy in Living Cells. Anal Chem 2023. [PMID: 37330921 DOI: 10.1021/acs.analchem.3c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The ability to monitor changes in metabolites and corresponding gene transcription within living cells is highly desirable. However, most current assays for quantification of metabolites or for gene transcription are destructive, precluding tracking the real-time dynamics of living cells. Here, we used the intracellular elemental sulfur in a Thiophaeococcus mangrovi cell as a proof-of-concept to link the quantity of metabolites and relevant gene transcription in living cells by a nondestructive Raman approach. Raman spectroscopy was utilized to quantify intracellular elemental sulfur noninvasively, and a computational mRR (mRNA and Raman) model was developed to infer the transcription of genes relevant to elemental sulfur. The results showed a significant linear correlation between the exponentially transformed Raman spectral intensity of intracellular elemental sulfur and the mRNA levels of genes encoding sulfur globule proteins in T. mangrovi. The mRR model was verified independently in two genera of Thiocapsa and Thiorhodococcus, and the mRNA levels predicted by mRR showed high consistency with actual gene expression detected by real-time polymerase chain reaction (PCR). This approach could enable noninvasive assessment of the quantity of metabolites and link the pertinent gene expression profiles in living cells, providing useful baseline data to spectroscopically map various omics in real time.
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Affiliation(s)
- Weilai Lu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Lu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Nosalova L, Piknova M, Kolesarova M, Pristas P. Cold Sulfur Springs-Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria. Microorganisms 2023; 11:1436. [PMID: 37374938 DOI: 10.3390/microorganisms11061436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa.
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Affiliation(s)
- Lea Nosalova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Maria Piknova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Mariana Kolesarova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Peter Pristas
- Centre of Biosciences, Institute of Animal Physiology, Slovak Academy of Sciences, 040 01 Kosice, Slovakia
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Ding W, Wang S, Qin P, Fan S, Su X, Cai P, Lu J, Cui H, Wang M, Shu Y, Wang Y, Fu HH, Zhang YZ, Li YX, Zhang W. Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms. Nat Commun 2023; 14:2033. [PMID: 37041201 PMCID: PMC10090131 DOI: 10.1038/s41467-023-37759-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/30/2023] [Indexed: 04/13/2023] Open
Abstract
Thiosulfate oxidation by microbes has a major impact on global sulfur cycling. Here, we provide evidence that bacteria within various Roseobacter lineages are important for thiosulfate oxidation in marine biofilms. We isolate and sequence the genomes of 54 biofilm-associated Roseobacter strains, finding conserved sox gene clusters for thiosulfate oxidation and plasmids, pointing to a niche-specific lifestyle. Analysis of global ocean metagenomic data suggests that Roseobacter strains are abundant in biofilms and mats on various substrates, including stones, artificial surfaces, plant roots, and hydrothermal vent chimneys. Metatranscriptomic analysis indicates that the majority of active sox genes in biofilms belong to Roseobacter strains. Furthermore, we show that Roseobacter strains can grow and oxidize thiosulfate to sulfate under both aerobic and anaerobic conditions. Transcriptomic and membrane proteomic analyses of biofilms formed by a representative strain indicate that thiosulfate induces sox gene expression and alterations in cell membrane protein composition, and promotes biofilm formation and anaerobic respiration. We propose that bacteria of the Roseobacter group are major thiosulfate-oxidizers in marine biofilms, where anaerobic thiosulfate metabolism is preferred.
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Affiliation(s)
- Wei Ding
- College of Marine Life Sciences and MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, China
| | - Shougang Wang
- College of Marine Life Sciences and MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Peng Qin
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Shen Fan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiaoyan Su
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Peiyan Cai
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, China
| | - Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Han Cui
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Meng Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yi Shu
- College of Marine Life Sciences and MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Yongming Wang
- College of Marine Life Sciences and MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Hui-Hui Fu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yu-Zhong Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.
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Whaley-Martin KJ, Chen LX, Nelson TC, Gordon J, Kantor R, Twible LE, Marshall S, McGarry S, Rossi L, Bessette B, Baron C, Apte S, Banfield JF, Warren LA. O 2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters. Nat Commun 2023; 14:2006. [PMID: 37037821 PMCID: PMC10086054 DOI: 10.1038/s41467-023-37426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/14/2023] [Indexed: 04/12/2023] Open
Abstract
The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we investigate biological sulfur oxidation over four years in a mine tailings impoundment water cap, integrating aqueous sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. The microbial community is consistently dominated by neutrophilic, chemolithoautotrophic SOB (relative abundances of ~76% in 2015, ~55% in 2016/2017 and ~60% in 2018). Results reveal two SOB strategies alternately dominate across the four years, influencing acid generation and sulfur speciation. Under oxic conditions, novel Halothiobacillus drive lower pH conditions (as low as 4.3) and lower [S2O32-] via the complete Sox pathway coupled to O2. Under anoxic conditions, Thiobacillus spp. dominate in activity, via the incomplete Sox and rDSR pathways coupled to NO3-, resulting in higher [S2O32-] and no net significant acidity generation. This study provides genomic evidence explaining acidity generation and thiosulfate accumulation patterns in a circumneutral mine tailing impoundment and has significant environmental applications in preventing the discharge of sulfur compounds that can impact downstream environments. These insights illuminate opportunities for in situ biotreatment of reduced sulfur compounds and prediction of acidification events using gene-based monitoring and in situ RNA detection.
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Affiliation(s)
- Kelly J Whaley-Martin
- University of Toronto, Toronto, ON, Canada
- Environmental Resources management (ERM), Toronto, ON, Canada
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | | | - Rose Kantor
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | - Stephanie Marshall
- Environmental Resources management (ERM), Toronto, ON, Canada
- McMaster University, Hamilton, ON, Canada
| | - Sam McGarry
- Glencore, Sudbury Integrated Nickel Operations, Sudbury, ON, Canada
| | | | | | | | - Simon Apte
- CSIRO Land and Water, Clayton, NSW, Australia
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
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Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:ijms24076491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
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Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
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Wang S, Jiang L, Cui L, Alain K, Xie S, Shao Z. Transcriptome Analysis of Cyclooctasulfur Oxidation and Reduction by the Neutrophilic Chemolithoautotrophic Sulfurovum indicum from Deep-Sea Hydrothermal Ecosystems. Antioxidants (Basel) 2023; 12:antiox12030627. [PMID: 36978876 PMCID: PMC10045233 DOI: 10.3390/antiox12030627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Chemolithoautotrophic Campylobacterota are widespread and predominant in worldwide hydrothermal vents, and they are key players in the turnover of zero-valence sulfur. However, at present, the mechanism of cyclooctasulfur activation and catabolism in Campylobacterota bacteria is not clearly understood. Here, we investigated these processes in a hydrothermal vent isolate named Sulfurovum indicum ST-419. A transcriptome analysis revealed that multiple genes related to biofilm formation were highly expressed during both sulfur oxidation and reduction. Additionally, biofilms containing cells and EPS coated on sulfur particles were observed by SEM, suggesting that biofilm formation may be involved in S0 activation in Sulfurovum species. Meanwhile, several genes encoding the outer membrane proteins of OprD family were also highly expressed, and among them, gene IMZ28_RS00565 exhibited significantly high expressions by 2.53- and 7.63-fold changes under both conditions, respectively, which may play a role in sulfur uptake. However, other mechanisms could be involved in sulfur activation and uptake, as experiments with dialysis bags showed that direct contact between cells and sulfur particles was not mandatory for sulfur reduction activity, whereas cell growth via sulfur oxidation did require direct contact. This indirect reaction could be ascribed to the role of H2S and/or other thiol-containing compounds, such as cysteine and GSH, which could be produced in the culture medium during sulfur reduction. In the periplasm, the sulfur-oxidation-multienzyme complexes soxABXY1Z1 and soxCDY2Z2 are likely responsible for thiosulfate oxidation and S0 oxidation, respectively. In addition, among the four psr gene clusters encoding polysulfide reductases, only psrA3B3C3 was significantly upregulated under the sulfur reduction condition, implying its essential role in sulfur reduction. These results expand our understanding of the interactions of Campylobacterota with the zero-valence sulfur and their adaptability to deep-sea hydrothermal environments.
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Affiliation(s)
- Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
- Correspondence: (L.J.); (Z.S.)
| | - Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China
| | - Karine Alain
- CNRS, Université Brest, Ifremer, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France
| | - Shaobin Xie
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Correspondence: (L.J.); (Z.S.)
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Chaudhary S, Sindhu SS, Dhanker R, Kumari A. Microbes-mediated sulphur cycling in soil: Impact on soil fertility, crop production and environmental sustainability. Microbiol Res 2023; 271:127340. [PMID: 36889205 DOI: 10.1016/j.micres.2023.127340] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/06/2023] [Accepted: 02/18/2023] [Indexed: 03/08/2023]
Abstract
Reduction in soil fertility and depletion of natural resources due to current intensive agricultural practices along with climate changes are the major constraints for crop productivity and global food security. Diverse microbial populations' inhabiting the soil and rhizosphere participate in biogeochemical cycling of nutrients and thereby, improve soil fertility and plant health, and reduce the adverse impact of synthetic fertilizers on the environment. Sulphur is 4th most common crucial macronutrient required by all organisms including plants, animals, humans and microorganisms. Effective strategies are required to enhance sulphur content in crops for minimizing adverse effects of sulphur deficiency on plants and humans. Various microorganisms are involved in sulphur cycling in soil through oxidation, reduction, mineralization, and immobilization, and volatalization processes of diverse sulphur compounds. Some microorganisms possess the unique ability to oxidize sulphur compounds into plant utilizable sulphate (SO42-) form. Considering the importance of sulphur as a nutrient for crops, many bacteria and fungi involved in sulphur cycling have been characterized from soil and rhizosphere. Some of these microbes have been found to positively affect plant growth and crop yield through multiple mechanisms including the enhanced mobilization of nutrients in soils (i.e., sulphate, phosphorus and nitrogen), production of growth-promoting hormones, inhibition of phytopathogens, protection against oxidative damage and mitigation of abiotic stresses. Application of these beneficial microbes as biofertilizers may reduce the conventional fertilizer application in soils. However, large-scale, well-designed, and long-term field trials are necessary to recommend the use of these microbes for increasing nutrient availability for growth and yield of crop plants. This review discusses the current knowledge regarding sulphur deficiency symptoms in plants, biogeochemical cycling of sulphur and inoculation effects of sulphur oxidizing microbes in improving plant biomass and crop yield in different crops.
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Affiliation(s)
- Suman Chaudhary
- Research Associate, EBL Laboratory, ICAR-Central Institute of Research on Buffaloes, Hisar 125001, Haryana, India.
| | - Satyavir Singh Sindhu
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, Haryana, India.
| | - Rinku Dhanker
- International Institute of Veterinary, Education & Research, Bahuakbarpur, Rohtak 124001, Haryana, India.
| | - Anju Kumari
- Center of Food Science and Technology, CCS Haryana Agricultural University, Hisar 125004, Haryana, India.
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Hu L, Wang Y, Ci M, Long Y. Unravelling microbial drivers of the sulfate-reduction process inside landfill using metagenomics. CHEMOSPHERE 2023; 313:137537. [PMID: 36521740 DOI: 10.1016/j.chemosphere.2022.137537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/25/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Hydrogen sulfide (H2S) is one of the common landfill odor. This research demonstrates that the sulfate transformation behavior is significantly enhanced during the landfill process, accompanied by a shift in microbial structure. The relative abundance of dissimilatory sulfate reduction (DSR) and thiosulfate oxidation by SOX (sulfur-oxidation) complex gradually decreases through the landfill processes while the assimilatory sulfate reduction (ASR) demonstrates the opposite behavior. The major module for landfill sulfate reduction is ASR, accounting for 31.72% ± 2.84% of sulfate metabolism. Based on the functional genes for the sulfate pathway, the drivers for sulfate biotransformation in landfills were determined and further identified their contribution in the sulfate metabolism during landfill processes. Pseudomonas, Methylocaldum, Bacillus, Methylocystis and Hyphomicrobium were the top 5 contributors for ASR pathway, and only one genus Pseudomonas was found for DSR pathway. Among the 26 high-quality metagenome-assembled genomes of sulfate functional species, 24 were considered novel species for sulfuric metabolism. Overall, this study provides unique insight into the sulfate transformation process related to the H2S odor control in landfill management.
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Affiliation(s)
- Lifang Hu
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Yuqian Wang
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Manting Ci
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Instrumental Analysis Center, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Yuyang Long
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Instrumental Analysis Center, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.
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C-, N-, S-, and P-Substrate Spectra in and the Impact of Abiotic Factors on Assessing the Biotechnological Potential of Paracoccus pantotrophus. Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Modern biotechnology benefits from the introduction of novel chassis organisms in remedying the limitations of already-established strains. For this, Paracoccus pantotrophus was chosen for in-depth assessment. Its unique broad metabolism and robustness against abiotic stressors make this strain a well-suited chassis candidate. This study set out to comprehensively overview abiotic influences on the growth performance of five P. pantotrophus strains. These data can aid in assessing the suitability of this genus for chassis development by using the type strain as a preliminary model organism. The five P. pantotrophus strains DSM 2944T, DSM 11072, DSM 11073, DSM 11104, and DSM 65 were investigated regarding their growth on various carbon sources and other nutrients. Our data show a high tolerance against osmotic pressure for the type strain with both salts and organic osmolytes. It was further observed that P. pantotrophus prefers organic acids over sugars. All of the tested strains were able to grow on short-chain alkanes, which would make P. pantotrophus a candidate for bioremediation and the upcycling of plastics. In conclusion, we were able to gain insights into several P. pantotrophus strains, which will aid in further introducing this species, or even another species from this genus, as a candidate for future biotechnological processes.
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A metabolic puzzle: Consumption of C 1 compounds and thiosulfate in Hyphomicrobium denitrificans X T. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148932. [PMID: 36367491 DOI: 10.1016/j.bbabio.2022.148932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/17/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
Many obligately heterotrophic methylotrophs oxidize thiosulfate as an additional electron source during growth on C1 compounds. Although two different pathways of thiosulfate oxidation are implemented in Hyphomicrobium denitrificans XT, a pronounced negative effect on growth rate is observed when it is cultured in the simultaneous presence of methanol and thiosulfate. In this model organism, periplasmic thiosulfate dehydrogenase TsdA catalyzes formation of the dead-end product tetrathionate. By reverse genetics we verified the second pathway that also starts in the periplasm where SoxXA catalyzes the oxidative fusion of thiosulfate to SoxYZ, from which sulfate is released by SoxB. Sulfane sulfur is then further oxidized in the cytoplasm by the sulfur-oxidizing heterodisulfide reductase-like system (sHdr) which is produced constitutively in a strain lacking the transcriptional repressor sHdrR. When exposed to thiosulfate, the ΔshdrR strain exhibited a strongly reduced growth rate even without thiosulfate in the pre-cultures. When grown on methanol, cells exhibit significantly increased NAD+/NADH ratios in the presence of thiosulfate. In contrast, thiosulfate did not exert any negative effect on growth rate or increase NAD+ levels during growth on formate. On both C1 substrates, excretion of up to 0.5 mM sulfite as an intermediate of thiosulfate (2 mM) oxidation was recorded. Sulfite is known to form adducts with pyrroloquinoline quinone, the cofactor of periplasmic methanol dehydrogenase. We rationalize that this causes specific inhibition of methanol degradation in the presence of thiosulfate while formate metabolism in the cytoplasm remains unaffected.
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Wang T, Huang Q, Burns AS, Moran MA, Whitman WB. Oxidative Stress Regulates a Pivotal Metabolic Switch in Dimethylsulfoniopropionate Degradation by the Marine Bacterium Ruegeria pomeroyi. Microbiol Spectr 2022; 10:e0319122. [PMID: 36301115 PMCID: PMC9769926 DOI: 10.1128/spectrum.03191-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/03/2022] [Indexed: 01/10/2023] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is an abundant organic compound in marine surface water and source of dimethyl sulfide (DMS), the largest natural sulfur source to the upper atmosphere. Marine bacteria either mineralize DMSP through the demethylation pathway or transform it to DMS through the cleavage pathway. Factors that regulate which pathway is utilized are not fully understood. In chemostat experiments, the marine Roseobacter Ruegeria pomeroyi DSS-3 was exposed to oxidative stress either during growth with H2O2 or by mutation of the gene encoding catalase. Oxidative stress reduced expression of the genes in the demethylation pathway and increased expression of those encoding the cleavage pathway. These results are contrary to the sulfur demand hypothesis, which theorizes that DMSP metabolism is driven by sulfur requirements of bacterial cells. Instead, we find strong evidence consistent with oxidative stress control over the switch in DMSP metabolism from demethylation to DMS production in an ecologically relevant marine bacterium. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is the most abundant low-molecular-weight organic compound in marine surface water and source of dimethyl sulfide (DMS), a climatically active gas that connects the marine and terrestrial sulfur cycles. Marine bacteria are the major DMSP consumers, either generating DMS or consuming DMSP as a source of reduced carbon and sulfur. However, the factors regulating the DMSP catabolism in bacteria are not well understood. Marine bacteria are also exposed to oxidative stress. RNA sequencing (RNA-seq) experiments showed that oxidative stress induced in the laboratory reduced expression of the genes encoding the consumption of DMSP via the demethylation pathway and increased the expression of genes encoding DMS production via the cleavage pathway in the marine bacterium Ruegeria pomeroyi. These results support a model where DMS production in the ocean is regulated in part by oxidative stress.
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Affiliation(s)
- Tao Wang
- Department of Microbiology, University of Georgia, Georgia, USA
| | - Qiuyuan Huang
- Department of Microbiology, University of Georgia, Georgia, USA
| | - Andrew S. Burns
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
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Han S, Li Y, Gao H. Generation and Physiology of Hydrogen Sulfide and Reactive Sulfur Species in Bacteria. Antioxidants (Basel) 2022; 11:antiox11122487. [PMID: 36552695 PMCID: PMC9774590 DOI: 10.3390/antiox11122487] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Sulfur is not only one of the most abundant elements on the Earth, but it is also essential to all living organisms. As life likely began and evolved in a hydrogen sulfide (H2S)-rich environment, sulfur metabolism represents an early form of energy generation via various reactions in prokaryotes and has driven the sulfur biogeochemical cycle since. It has long been known that H2S is toxic to cells at high concentrations, but now this gaseous molecule, at the physiological level, is recognized as a signaling molecule and a regulator of critical biological processes. Recently, many metabolites of H2S, collectively called reactive sulfur species (RSS), have been gradually appreciated as having similar or divergent regulatory roles compared with H2S in living organisms, especially mammals. In prokaryotes, even in bacteria, investigations into generation and physiology of RSS remain preliminary and an understanding of the relevant biological processes is still in its infancy. Despite this, recent and exciting advances in the fields are many. Here, we discuss abiotic and biotic generation of H2S/RSS, sulfur-transforming enzymes and their functioning mechanisms, and their physiological roles as well as the sensing and regulation of H2S/RSS.
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Wang L, Shen Z, Cheng X, Hwang JS, Guo Y, Sun M, Cao J, Liu R, Fang J. Metagenomic insights into the functions of microbial communities in sulfur-rich sediment of a shallow-water hydrothermal vent off Kueishan Island. Front Microbiol 2022; 13:992034. [DOI: 10.3389/fmicb.2022.992034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
Hydrothermal vent (HTV) systems are important habitats for understanding the biological processes of extremophiles on Earth and their relative contributions to material and energy cycles in the ocean. Current understanding on hydrothermal systems have been primarily focused on deep-sea HTVs, and little is known about the functions and metabolisms of microorganisms in shallow-water HTVs (SW-HTVs), which are distinguished from deep-sea HTVs by a depth limit of 200 m. In this study, we analyzed metagenomes of sulfur-rich sediment samples collected from a SW-HTV of Kueishan Island, located in a marginal sea of the western Pacific Ocean. Comparing with a previously published report of pelagic samples from the nearby sampling site, microbial communities in the SW-HTV sediments enriching with genes of both aerobic and anaerobic respiration inferred variable environments in the tested sediments. Abundant genes of energy metabolism encoding sulfur oxidation, H2 oxidation, and carbon fixation were detected from the sediment samples. Sixty-eight metagenome-assembled-genomes (MAGs) were reconstructed to further understand the metabolism and potential interactions between different microbial taxa in the SW-HTVs sediment. MAGs with the highest abundant were chemolithotrophic sulfur-oxidization bacteria, including Sulfurovum represented Campylobacteria involved sox multienzyme, sulfide oxidation genes and rTCA cycle, and Gammaproteobacteria involved dsr gene and CBB cycle. In addition, Desulfobacterota with the potential to participate in sulfur-disproportionating processes also had higher abundance than the sample’s overall mean value. The interaction of these bacterial groups allows the microbial communities to efficiently metabolize a large variety of sulfur compounds. In addition, the potential to use simple organic carbon, such as acetate, was found in chemolithotrophic Campylobacterial MAGs. Collectively, our results revealed the complexity of environmental conditions of the vent sediment and highlight the interactive relationships of the dominant microbial populations in driving sulfur cycles in the SW-HTV sediments off Kueishan Island.
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Marimuthu J, Rangamaran VR, Subramanian SHS, Balachandran KRS, Thenmozhi Kulasekaran N, Vasudevan D, Lee JK, Ramalingam K, Gopal D. Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance. Genomics 2022; 114:110524. [PMID: 36423774 DOI: 10.1016/j.ygeno.2022.110524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/06/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022]
Abstract
Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.
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Affiliation(s)
- Jeya Marimuthu
- Marine Biotechnology Division, National Institute of Ocean Technology, Chennai 600100, India.
| | | | | | | | | | - Dinakaran Vasudevan
- KMCH Research Foundation, Coimbatore Medical Center and Hospital, Coimbatore 641014, India
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 143 701, Republic of Korea
| | - Kirubagaran Ramalingam
- Marine Biotechnology Division, National Institute of Ocean Technology, Chennai 600100, India
| | - Dharani Gopal
- Marine Biotechnology Division, National Institute of Ocean Technology, Chennai 600100, India.
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Deng YF, Zan FX, Huang H, Wu D, Tang WT, Chen GH. Coupling sulfur-based denitrification with anammox for effective and stable nitrogen removal: A review. WATER RESEARCH 2022; 224:119051. [PMID: 36113234 DOI: 10.1016/j.watres.2022.119051] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/15/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Anoxic ammonium oxidation (anammox) is an energy-efficient nitrogen removal process for wastewater treatment. However, the unstable nitrite supply and residual nitrate in the anammox process have limited its wide application. Recent studies have proven coupling of sulfur-based denitrification with anammox (SDA) can achieve an effective nitrogen removal, owing to stable provision of substrate nitrite from the sulfur-based denitrification, thus making its process control more efficient in comparison with that of partial nitrification and anammox process. Meanwhile, the anammox-produced nitrate can be eliminated through sulfur-based denitrification, thereby enhancing SDA's overall nitrogen removal efficiency. Nonetheless, this process is governed by a complex microbial system that involves both complicated sulfur and nitrogen metabolisms as well as multiple interactions among sulfur-oxidising bacteria and anammox bacteria. A comprehensive understanding of the principles of the SDA process is the key to facilitating the development and application of this novel process. Hence, this review is conducted to systematically summarise various findings on the SDA process, including its associated biochemistry, biokinetic reactions, reactor performance, and application. The dominant functional bacteria and microbial interactions in the SDA process are further discussed. Finally, the advantages, challenges, and future research perspectives of SDA are outlined. Overall, this work gives an in-depth insight into the coupling mechanism of SDA and its potential application in biological nitrogen removal.
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Affiliation(s)
- Yang-Fan Deng
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China
| | - Fei-Xiang Zan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Huang
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China
| | - Di Wu
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Center for Environmental and Energy Research, Ghent University Global Campus, Republic of Korea
| | - Wen-Tao Tang
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China.
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Torgeson JM, Rosenfeld CE, Dunshee AJ, Duhn K, Schmitter R, O'Hara PA, Ng GHC, Santelli CM. Hydrobiogechemical interactions in the hyporheic zone of a sulfate-impacted, freshwater stream and riparian wetland ecosystem. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1360-1382. [PMID: 35661843 DOI: 10.1039/d2em00024e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Coupled abiotic and biotic processes in the hyporheic zone, where surface water and groundwater mix, play a critical role in the biogeochemical cycling of carbon, nutrients, and trace elements in streams and wetlands. Dynamic hydrologic conditions and anthropogenic pollution can impact redox gradients and biogeochemical response, although few studies examine the resulting hydrobiogeochemical interactions generated within the hyporheic zone. This study examines the effect of hyporheic flux dynamics and anthropogenic sulfate loading on the biogeochemistry of a riparian wetland and stream system. The hydrologic gradient as well as sediment, surface water, and porewater geochemistry chemistry was characterized at multiple points throughout the 2017 spring-summer-fall season at a sulfate-impacted stream flanked by wetlands in northern Minnesota. Results show that organic-rich sediments largely buffer the geochemical responses to brief or low magnitude changes in hydrologic gradient, but sustained or higher magnitude fluxes may variably alter the redox regime and, ultimately, the environmental geochemistry. This has implications for a changing climate that is expected to dramatically alter the hydrological cycle. Further, increased sulfate loading and dissolved or adsorbed ferric iron complexes in the hyporheic zone may induce a cryptic sulfur cycle linked to iron and carbon cycling, as indicated by the abundance of intermediate valence sulfur compounds (e.g., polysulfide, elemental sulfur, thiosulfate) throughout the anoxic wetland and stream-channel sediment column. The observed deviation from a classical redox tower coupled with potential changes in hydraulic gradient in these organic-rich wetland and stream hyporheic zones has implications for nutrient, trace element, and greenhouse gas fluxes into surface water and groundwater, ultimately influencing water quality and global climate.
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Affiliation(s)
- Joshua M Torgeson
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Carla E Rosenfeld
- Section of Minerals and Earth Sciences, Carnegie Museum of Natural History, USA.
| | - Aubrey J Dunshee
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Kelly Duhn
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
| | - Riley Schmitter
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Patrick A O'Hara
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - G H Crystal Ng
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
- St. Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cara M Santelli
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
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Yang Y, Perez Calleja P, Liu Y, Nerenberg R, Chai H. Assessing Intermediate Formation and Electron Competition during Thiosulfate-Driven Denitrification: An Experimental and Modeling Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11760-11770. [PMID: 35921133 DOI: 10.1021/acs.est.2c03937] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
There is increasing interest in thiosulfate-driven denitrification for low C/N wastewater treatment, but the denitrification performance varies with the thiosulfate oxidation pathways. Models have been developed to predict the products of denitrification, but few consider thiosulfate reduction to elemental sulfur (S0), an undesirable reaction that can intensify electron competition with denitrifying enzymes. In this study, the model using indirect coupling of electrons (ICE) was developed to predict S0 formation and electron competition during thiosulfate-driven denitrification. Kinetic data were obtained from sulfur-oxidizing bacteria (SOB) dominated by the branched pathway and were used to calibrate and validate the model. Electron competition was investigated under different operating conditions. Modeling results reveal that electrons produced in the first step of thiosulfate oxidation typically prioritize thiosulfate reduction, then nitrate reduction, and finally nitrite reduction. However, the electron consumption rate for S0 formation decreases sharply with the decline of thiosulfate concentration. Thus, a continuous feeding strategy was effective in alleviating the competition between thiosulfate reduction and denitrifying enzymes. Electron competition leads to nitrite accumulation, which could be a reliable substrate for anammox. The model was further evaluated with anammox integration. Results suggested that the branched pathway and continuous supply of thiosulfate are favorable to create a symbiotic relationship between SOB and anammox.
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Affiliation(s)
- Yan Yang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Patricia Perez Calleja
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Yiwen Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, PR China
| | - Robert Nerenberg
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Hongxiang Chai
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
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Venturini AM, Gontijo JB, Mandro JA, Paula FS, Yoshiura CA, da França AG, Tsai SM. Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils. Microb Genom 2022; 8. [PMID: 35894927 PMCID: PMC9455692 DOI: 10.1099/mgen.0.000853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.
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Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, USA
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Jéssica A Mandro
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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Complete genome sequence of Pseudomonas stutzeri S116 owning bifunctional catalysis provides insights into affecting performance of microbial fuel cells. BMC Microbiol 2022; 22:137. [PMID: 35590268 PMCID: PMC9118636 DOI: 10.1186/s12866-022-02552-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 05/03/2022] [Indexed: 12/03/2022] Open
Abstract
Background Pseudomonas stutzeri S116 is a sulfur-oxidizing bacteria isolated from marine sludge. It exhibited excellent electricity generation as bioanode and biocathode applied in microbial fuel cells (MFCs). Complete genome sequencing of P. stutzeri and cyclic voltammetry method were performed to reveal its mechanism in microbial fuel cells system. Results This study indicated that the MFCs generated a maximum output voltage of 254.2 mV and 226.0 mV, and maximum power density of 765 mW/m2 and 656.6 mW/m2 respectively. Complete genome sequencing of P. stutzeri S116 was performed to indicate that most function genes showed high similarities with P. stutzeri, and its primary annotations were associated with energy production and conversion (6.84%), amino acid transport and metabolism (6.82%) and inorganic ion transport and metabolism (6.77%). Homology of 36 genes involved in oxidative phosphorylation was detected, which suggests the strain S116 possesses an integrated electron transport chain. Additionally, many genes encoding pilus-assembly proteins and redox mediators (riboflavin and phenazine) were detected in the databases. Thiosulfate oxidization and dissimilatory nitrate reduction were annotated in the sulfur metabolism pathway and nitrogen metabolism pathway, respectively. Gene function analysis and cyclic voltammetry indicated that P. stutzeri probably possesses cellular machinery such as cytochrome c and redox mediators and can perform extracellular electron transfer and produce electricity in MFCs. Conclusion The redox mediators secreted by P. stutzeri S116 were probably responsible for performance of MFCs. The critical genes and metabolic pathways involved in thiosulfate oxide and nitrate reduction were detected, which indicated that the strain can treat wastewater containing sulfide and nitrite efficiently. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02552-8.
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45
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Tanabe TS, Dahl C. HMS-S-S: a tool for the identification of sulfur metabolism-related genes and analysis of operon structures in genome and metagenome assemblies. Mol Ecol Resour 2022; 22:2758-2774. [PMID: 35579058 DOI: 10.1111/1755-0998.13642] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/25/2022] [Accepted: 05/11/2022] [Indexed: 11/26/2022]
Abstract
Sulfur compounds are used in a variety of biological processes including respiration and photosynthesis. Sulfide and sulfur compounds of intermediary oxidation state can serve as electron donors for lithotrophic growth while sulfate, thiosulfate and sulfur are used as electron acceptors in anaerobic respiration. The biochemistry underlying the manifold transformations of inorganic sulfur compounds occurring in sulfur metabolizing prokaryotes is astonishingly complex and knowledge about it has immensely increased over the last years. The advent of next-generation sequencing approaches as well as the significant increase of data availability in public databases has driven focus of environmental microbiology to probing the metabolic capacity of microbial communities by analysis of this sequence data. To facilitate these analyses, we created HMS-S-S, a comprehensive equivalogous hidden Markov model (HMM)-supported tool. Protein sequences related to sulfur compound oxidation, reduction, transport and intracellular transfer are efficiently detected and related enzymes involved in dissimilatory sulfur oxidation as opposed to sulfur compound reduction can be confidently distinguished. HMM search results are coupled to corresponding genes, which allows analysis of co-occurrence, synteny and genomic neighborhood. The HMMs were validated on an annotated test dataset and by cross-validation. We also proved its performance by exploring meta-assembled genomes isolated from samples from environments with active sulfur cycling, including members of the cable bacteria, novel Acidobacteria and assemblies from a sulfur-rich glacier, and were able to replicate and extend previous reports.
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Affiliation(s)
- Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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46
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Yin X, Wang W, Wang A, He M, Lin C, Ouyang W, Liu X. Microbial community structure and metabolic potential in the coastal sediments around the Yellow River Estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151582. [PMID: 34785215 DOI: 10.1016/j.scitotenv.2021.151582] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
The Yellow River Estuary and Laizhou Bay are located on the northern Shandong Peninsula in the Bohai Sea in China and have been polluted by intensive anthropogenic activity. However, few studies have focused on the effect of these activities on the microbial communities and their ecological functions in this area. In this study, the combination of 16S rDNA gene sequencing and GeoChip technology was used to analyzed the microbial community component and their functional genes. Thaumarchaeot and Bacteroidetes are the most abundant phyla. The results of correlation analysis and redundancy analysis (RDA) showed water depth (r2 = 0.76, P = 0.005), total Na content (r2 = 0.63, P = 0.021) and total Ca content (r2 = 0.53, P = 0.05) in the sediments were the most significant environmental factors affecting the microbial community. The diversity of the microbial community and signal intensity of functional genes at nearshore sites (N sites) were higher than that at the offshore sites (O sites), but the component of microbial community and functional genes was similar in general. Functional genes for C, N, P and S cycle were detected at both nearshore and offshore sites, which illustrated that microbial communities were active in nutrient cycle. Proteobacteria contributes significantly to material cycle in microbial community. In addition, functional genes related to organic remediation and metal detoxification are also abundant. It indicated that the environmental pollution caused by anthropogenic activities has greatly affected the microbial community components and their biochemical functions in the Yellow River Estuary and surrounding areas. This study reveals the effect of anthropogenic activities on microbial communities and provides the basis for environmental management.
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Affiliation(s)
- Xiaobo Yin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wenting Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Aihua Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Chunye Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Ouyang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xitao Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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Oliver JAW, Kelbrick M, Ramkissoon NK, Dugdale A, Stephens BP, Kucukkilic-Stephens E, Fox-Powell MG, Schwenzer SP, Antunes A, Macey MC. Sulfur Cycling as a Viable Metabolism under Simulated Noachian/Hesperian Chemistries. Life (Basel) 2022; 12:life12040523. [PMID: 35455014 PMCID: PMC9024814 DOI: 10.3390/life12040523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 12/17/2022] Open
Abstract
Water present on the surface of early Mars (>3.0 Ga) may have been habitable. Characterising analogue environments and investigating the aspects of their microbiome best suited for growth under simulated martian chemical conditions is key to understanding potential habitability. Experiments were conducted to investigate the viability of microbes from a Mars analogue environment, Colour Peak Springs (Axel Heiberg Island, Canadian High Arctic), under simulated martian chemistries. The fluid was designed to emulate waters thought to be typical of the late Noachian, in combination with regolith simulant material based on two distinct martian geologies. These experiments were performed with a microbial community from Colour Peak Springs sediment. The impact on the microbes was assessed by cell counting and 16S rRNA gene amplicon sequencing. Changes in fluid chemistries were tested using ICP-OES. Both chemistries were shown to be habitable, with growth in both chemistries. Microbial communities exhibited distinct growth dynamics and taxonomic composition, comprised of sulfur-cycling bacteria, represented by either sulfate-reducing or sulfur-oxidising bacteria, and additional heterotrophic halophiles. Our data support the identification of Colour Peak Springs as an analogue for former martian environments, with a specific subsection of the biota able to survive under more accurate proxies for martian chemistries.
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Affiliation(s)
- James A. W. Oliver
- Biology Department, Edge Hill University, Ormskirk L39 4QP, UK; (J.A.W.O.); (M.K.)
| | - Matthew Kelbrick
- Biology Department, Edge Hill University, Ormskirk L39 4QP, UK; (J.A.W.O.); (M.K.)
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3GJ, UK
| | - Nisha K. Ramkissoon
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - Amy Dugdale
- AstrobiologyOU, School of Physical Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK;
- Biology Department, Maynooth University, Maynooth, W23 F2H6 Kildare, Ireland
| | - Ben P. Stephens
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - Ezgi Kucukkilic-Stephens
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - Mark G. Fox-Powell
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
- School of Earth & Environmental Sciences, University of St Andrews, Fife KY16 9AJ, UK
| | - Susanne P. Schwenzer
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, China;
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Macau, China
| | - Michael C. Macey
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
- Correspondence:
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Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state. THE ISME JOURNAL 2022; 16:972-982. [PMID: 34743175 PMCID: PMC8940887 DOI: 10.1038/s41396-021-01143-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/08/2022]
Abstract
Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.
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Metabolism of the Genus Guyparkeria Revealed by Pangenome Analysis. Microorganisms 2022; 10:microorganisms10040724. [PMID: 35456775 PMCID: PMC9032823 DOI: 10.3390/microorganisms10040724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 02/04/2023] Open
Abstract
Halophilic sulfur-oxidizing bacteria belonging to the genus Guyparkeria occur at both marine and terrestrial habitats. Common physiological characteristics displayed by Guyparkeria isolates have not yet been linked to the metabolic potential encoded in their genetic inventory. To provide a genetic basis for understanding the metabolism of Guyparkeria, nine genomes were compared to reveal the metabolic capabilities and adaptations. A detailed account is given on Guyparkeria’s ability to assimilate carbon by fixation, to oxidize reduced sulfur, to oxidize thiocyanate, and to cope with salinity stress.
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Huang Y, Wang B, Yang Y, Yang S, Dong M, Xu M. Microbial carriers promote and guide pyrene migration in sediments. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127188. [PMID: 34597936 DOI: 10.1016/j.jhazmat.2021.127188] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Microbial carriers may co-transport polycyclic aromatic hydrocarbons (PAHs), but lack substantial experimental evidence. Cable bacteria use gliding or twitching motility to access sulfide; hence, they could be important microbial carriers in co-transporting PAHs from the sediment-water interface into suboxic zones. In this study, the effect of cable bacteria on pyrene migration was investigated by connecting or blocking the paths of cable bacteria to the suboxic zones. The results showed that downward migration of pyrene in the connecting groups were significantly higher (17.3-49.2%, p < 0.01) than those in the control groups. Meanwhile, significant downward migration of microbial communities in the connecting groups were also observed, including abundant filamentous-motile microorganisms, especially cable bacteria. The adsorption of surrounding particles by cable bacteria were morphologically evidenced. The biomechanical model based on the Peclet number indicated that filamentous-motile microorganisms demonstrated stronger adsorption ability for pyrene than other microorganisms. Supposedly, the downward migration of microbial communities, especially cable bacteria, significantly enhanced pyrene migration, thus influencing the distribution and ecological risk of pyrene in sediments. This study provides new insights into the important roles of motile microorganisms in the migration of PAHs in sediments, shedding lights on guidance for ecological risk assessment of PAHs.
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Affiliation(s)
- Youda Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Meijun Dong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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